Just to throw my $0.02Cdn in, and since we're talking about a new game (boy it's good ta see ya Harry!) my take would be a bit of both and a bit of neither.
If we're talking about future computer-based targetting systems (as dave leaps into unreality for a moment) I'd assume we're balancing two things: detecting/targetting the opponent while preventing them from getting a good shot at you. So, perhaps the following:
(1) each type of ship has basic detection and evasion properties (not the best use of terminology, but ya get my drift) ,
these could be customized to a limited extent in dock by the acquisition of better hardware, software, and crew
(2) during combat, the energy signature and specific actions of the ship also make it easier/more difficult to target -- actively boosting your own targetting systems also makes you easier to target, as does firing weapons, the amount of power you have shoved into the shields would make you more/less visibile, the amount of impulse power you're throwing out, etc etc.
As a captain, you're deciding what actions to take for a better lock on the enemy vs what kind of a target that will make you - I'd assume the computers are taking into account everything they can otherwise - with the added catch that of course you really don't know how good the other fella's systems/crew are.
The number and extent of the influencing factors is pretty much up for grabs, I wouldn't want to be the one writing the rule set on how all the different systems should interact tho
Anyway, hope that made sense (been a long day!)
dave